Constant errors with Rigify (Blender), and ultimately can't import to Unity3D
Go into Blender's User Preferences and on the File menu, tick 'Auto Run Python Scripts' on and regenerate the rig. This will fix half of it missing. However, when you move into Unity, you'll notice that Rigify creates a lot of controllers and widgets, that while very helpful in Blender, are rubbish for Unity. I suggest taking a look at the Rigify to Unity package in the Asset Store as well.